A technique called MS/MS analysis (MS2 analysis) has been known in the field of mass spectrometry using an ion trap-type mass spectrometer. In general MS2 analysis, first a target ion having a specific mass-to-charge ratio (m/z) is selected from the unknown compound to be analyzed as a precursor ion (parent ion) and the selected precursor ion is fragmented through collision induced disassociation (CID) so as to generated fragmented ions. The manner in which the ion fragments depends on the chemical structure and, therefore, the MS2 mass spectrum of the unknown compound (information on the chemical structure) can be acquired through mass spectrometry of the fragmented ions that have been generated through fragmentation.
In recent years, unknown compounds to be identified, such as of a medicine, of a pesticide or of a protein, have a large molecular weight and also have a complicated chemical structure. Therefore, in some cases, ions do not fragment into fragmented ions having a sufficiently small mass using only a one-step fragmenting operation depending on the type of the unknown compound. In such a case, the fragmenting operation is repeated a number of times and, thus, mass spectrometry is carried out on the generated fragmented ions through MSn analysis.
A pattern matching process using a data base has been carried out as an analysis process for estimating the chemical structure of the unknown compound from the MSn mass spectrum gained through the above described MSn analysis (see Patent Document 1 and Non-Patent Document 1). The data base includes the names and the chemical structures of a great number of compounds (known compounds) and the MSn mass spectra of these known compounds. In the pattern matching process the MSn mass spectra of the known compounds and the MSn mass spectrum of an unknown compound are compared so as to find the respective scores indicating similarities between the MSn mass spectrum of the unknown compound and the MSn mass spectra of the great number of known compounds using weighted inner products and the probabilities of occurrences of peaks. As a result, the unknown compounds are aligned in the descending order of scores and, thus, the person conducting the measurement identifies the unknown compound.